Genome-wide somatic variants in CRC (GRCh38)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006572	The dataset contains somatic variants in 344 colorectal cancer samples. Variants are called with Mutect2 (GRCh38). Important: VCF-files include also variants, which have been annotated as "str_contraction" and "panel_of_normals". Please, use only "PASS" variants in studies, which are not microsatellite repeat related. Samples are sequenced with Novaseq 6000, HiSeq 2000, and HiSeq X Ten instruments (average coverage depth ~30+). The dataset consists of 257 MSS, 58 MSI, 25 MSS IBD, and 4 POLE mutant CRCs.		344

Publications	Citations
Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. Sanjaya P, Maljanen K, Katainen R, Waszak SM, Genomics England Research Consortium, Aaltonen LA, Stegle O, Korbel JO, Pitkänen E. Genome Med 15: 2023 47	15
Lynch syndrome-associated and sporadic microsatellite unstable colorectal cancers: different patterns of clonal evolution yield highly similar tumours. Martin S, Katainen R, Taira A, Välimäki N, Ristimäki A, Seppälä T, Renkonen-Sinisalo L, Lepistö A, Tahkola K, Mattila A, Koskensalo S, Mecklin JP, Rajamäki K, Palin K, Aaltonen LA. Hum Mol Genet 33: 2024 1858-1872	7
Comprehensive metabolomic and epigenomic characterization of microsatellite stable BRAF-mutated colorectal cancer. Taira A, Aavikko M, Katainen R, Kaasinen E, Välimäki N, Ravantti J, Ristimäki A, Seppälä TT, Renkonen-Sinisalo L, Lepistö A, Tahkola K, Mattila A, Koskensalo S, Mecklin JP, Böhm J, Bramsen JB, Andersen CL, Palin K, Rajamäki K, Aaltonen LA, iCAN. Oncogene 44: 2025 1718-1730	1